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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-06-03, 22:34 PDT based on data in: /hb/groups/kelley_lab/tina/mytilus/02_trim/final_trim0603/concat/fastqc


        General Statistics

        Showing 174/174 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        12O-F_S66_R1_merged
        66.3%
        27%
        0.7M
        12O-F_S66_R2_merged
        68.2%
        25%
        0.7M
        12O-G_S22_R1_merged
        59.1%
        29%
        0.7M
        12O-G_S22_R2_merged
        60.5%
        28%
        0.7M
        14B-F_S71_R1_merged
        42.9%
        28%
        0.1M
        14B-F_S71_R2_merged
        43.8%
        27%
        0.1M
        14B-G_S25_R1_merged
        63.7%
        26%
        1.1M
        14B-G_S25_R2_merged
        64.0%
        25%
        1.1M
        15G-F_S52_R1_merged
        77.1%
        29%
        1.7M
        15G-F_S52_R2_merged
        78.6%
        27%
        1.7M
        15G-G_S24_R1_merged
        52.4%
        26%
        0.4M
        15G-G_S24_R2_merged
        53.4%
        25%
        0.4M
        15W-G_S12_R1_merged
        38.9%
        28%
        0.1M
        15W-G_S12_R2_merged
        39.1%
        27%
        0.1M
        160-G_S11_R1_merged
        29.9%
        25%
        0.2M
        160-G_S11_R2_merged
        30.0%
        24%
        0.2M
        16O-G_S62_R1_merged
        58.0%
        27%
        0.5M
        16O-G_S62_R2_merged
        58.6%
        26%
        0.5M
        18W-F_S81_R1_merged
        30.7%
        30%
        0.0M
        18W-F_S81_R2_merged
        31.1%
        29%
        0.0M
        18W-G_S41_R1_merged
        48.1%
        30%
        0.8M
        18W-G_S41_R2_merged
        48.7%
        29%
        0.8M
        20G-F_S2_R1_merged
        58.9%
        26%
        0.5M
        20G-F_S2_R2_merged
        60.3%
        24%
        0.5M
        20G-G_S29_R1_merged
        72.6%
        27%
        1.1M
        20G-G_S29_R2_merged
        73.1%
        26%
        1.1M
        21B-F_S54_R1_merged
        56.6%
        28%
        0.2M
        21B-F_S54_R2_merged
        57.3%
        27%
        0.2M
        21B-G_S7_R1_merged
        73.2%
        28%
        1.9M
        21B-G_S7_R2_merged
        73.9%
        27%
        1.9M
        28W-F_S45_R1_merged
        52.9%
        29%
        0.2M
        28W-F_S45_R2_merged
        53.8%
        28%
        0.2M
        28W-G_S47_R1_merged
        36.4%
        27%
        0.2M
        28W-G_S47_R2_merged
        36.0%
        26%
        0.2M
        29W-G_S76_R1_merged
        52.3%
        28%
        0.8M
        29W-G_S76_R2_merged
        52.3%
        28%
        0.8M
        29Y-F_S74_R1_merged
        67.0%
        28%
        0.5M
        29Y-F_S74_R2_merged
        68.2%
        27%
        0.5M
        29Y-G_S68_R1_merged
        50.8%
        26%
        0.4M
        29Y-G_S68_R2_merged
        52.7%
        25%
        0.4M
        2B-F_S72_R1_merged
        54.1%
        32%
        0.4M
        2B-F_S72_R2_merged
        54.8%
        32%
        0.4M
        2B-G_S17_R1_merged
        68.5%
        28%
        1.2M
        2B-G_S17_R2_merged
        69.5%
        27%
        1.2M
        33G-F_S23_R1_merged
        38.4%
        32%
        0.1M
        33G-F_S23_R2_merged
        39.0%
        31%
        0.1M
        38B-F_S42_R1_merged
        39.3%
        30%
        0.3M
        38B-F_S42_R2_merged
        40.0%
        29%
        0.3M
        38B-G_S78_R1_merged
        40.8%
        30%
        0.1M
        38B-G_S78_R2_merged
        41.6%
        29%
        0.1M
        40Y-F_S84_R1_merged
        72.4%
        29%
        0.8M
        40Y-F_S84_R2_merged
        73.7%
        28%
        0.8M
        40Y-G_S63_R1_merged
        71.1%
        28%
        0.8M
        40Y-G_S63_R2_merged
        72.0%
        27%
        0.8M
        45G-F_S32_R1_merged
        76.2%
        27%
        1.7M
        45G-F_S32_R2_merged
        78.1%
        26%
        1.7M
        45G-G_S69_R1_merged
        72.1%
        27%
        1.1M
        45G-G_S69_R2_merged
        72.6%
        26%
        1.1M
        47W-F_S82_R1_merged
        62.1%
        28%
        0.4M
        47W-F_S82_R2_merged
        64.1%
        27%
        0.4M
        47W-G_S80_R1_merged
        66.2%
        28%
        1.0M
        47W-G_S80_R2_merged
        66.9%
        27%
        1.0M
        50B-G_S83_R1_merged
        66.0%
        27%
        1.4M
        50B-G_S83_R2_merged
        67.6%
        26%
        1.4M
        50G-F_S13_R1_merged
        58.0%
        27%
        0.5M
        50G-F_S13_R2_merged
        56.4%
        26%
        0.5M
        50G-G_S33_R1_merged
        69.4%
        28%
        0.9M
        50G-G_S33_R2_merged
        70.2%
        27%
        0.9M
        51B-G_S18_R1_merged
        70.2%
        28%
        1.3M
        51B-G_S18_R2_merged
        71.0%
        27%
        1.3M
        55B-F_S4_R1_merged
        58.4%
        28%
        0.6M
        55B-F_S4_R2_merged
        59.2%
        27%
        0.6M
        55B-G_S40_R1_merged
        55.6%
        27%
        1.2M
        55B-G_S40_R2_merged
        55.3%
        27%
        1.2M
        55Y-F_S61_R1_merged
        66.7%
        29%
        0.5M
        55Y-F_S61_R2_merged
        66.8%
        28%
        0.5M
        55Y-G_S10_R1_merged
        57.0%
        27%
        0.4M
        55Y-G_S10_R2_merged
        57.8%
        26%
        0.4M
        56Y-G_S53_R1_merged
        63.6%
        28%
        0.8M
        56Y-G_S53_R2_merged
        64.4%
        26%
        0.8M
        60G-F_S65_R1_merged
        71.0%
        26%
        1.5M
        60G-F_S65_R2_merged
        72.2%
        24%
        1.5M
        60G-G_S58_R1_merged
        43.5%
        28%
        0.2M
        60G-G_S58_R2_merged
        43.8%
        27%
        0.2M
        61W-F_S38_R1_merged
        55.8%
        29%
        0.3M
        61W-F_S38_R2_merged
        57.1%
        29%
        0.3M
        61W-G_S5_R1_merged
        51.1%
        31%
        0.3M
        61W-G_S5_R2_merged
        51.9%
        31%
        0.3M
        62W-F_S49_R1_merged
        45.7%
        27%
        0.2M
        62W-F_S49_R2_merged
        46.5%
        26%
        0.2M
        63G-F_S27_R1_merged
        50.4%
        29%
        0.1M
        63G-F_S27_R2_merged
        51.8%
        28%
        0.1M
        63G-G_S35_R1_merged
        60.3%
        27%
        0.7M
        63G-G_S35_R2_merged
        61.5%
        26%
        0.7M
        67B-F_S20_R1_merged
        50.2%
        31%
        0.6M
        67B-F_S20_R2_merged
        50.8%
        31%
        0.6M
        67B-G_S8_R1_merged
        72.0%
        27%
        2.3M
        67B-G_S8_R2_merged
        73.0%
        26%
        2.3M
        67W-F_S34_R1_merged
        40.2%
        30%
        0.1M
        67W-F_S34_R2_merged
        41.3%
        29%
        0.1M
        67W-G_S86_R1_merged
        63.1%
        26%
        1.1M
        67W-G_S86_R2_merged
        64.1%
        25%
        1.1M
        6O-F_S6_R1_merged
        62.1%
        27%
        0.4M
        6O-F_S6_R2_merged
        62.8%
        25%
        0.4M
        6W-F_S50_R1_merged
        75.0%
        28%
        1.4M
        6W-F_S50_R2_merged
        76.0%
        26%
        1.4M
        6W-G_S15_R1_merged
        66.8%
        28%
        0.3M
        6W-G_S15_R2_merged
        67.3%
        27%
        0.3M
        72Y-F_S28_R1_merged
        73.8%
        28%
        1.2M
        72Y-F_S28_R2_merged
        75.4%
        27%
        1.2M
        75Y-G_S9_R1_merged
        63.8%
        27%
        0.6M
        75Y-G_S9_R2_merged
        64.7%
        26%
        0.6M
        76Y-F_S46_R1_merged
        60.0%
        27%
        0.4M
        76Y-F_S46_R2_merged
        60.7%
        26%
        0.4M
        76Y-G_S85_R1_merged
        64.8%
        28%
        0.6M
        76Y-G_S85_R2_merged
        66.6%
        27%
        0.6M
        81G-F_S79_R1_merged
        69.8%
        28%
        0.8M
        81G-F_S79_R2_merged
        71.1%
        27%
        0.8M
        86G-F_S75_R1_merged
        77.4%
        26%
        2.3M
        86G-F_S75_R2_merged
        78.5%
        25%
        2.3M
        89Y-F_S31_R1_merged
        74.0%
        28%
        1.5M
        89Y-F_S31_R2_merged
        75.8%
        27%
        1.5M
        90W-F_S21_R1_merged
        49.1%
        28%
        0.6M
        90W-F_S21_R2_merged
        49.3%
        27%
        0.6M
        90W-G_S67_R1_merged
        61.5%
        28%
        0.4M
        90W-G_S67_R2_merged
        62.7%
        27%
        0.4M
        91W-F_S30_R1_merged
        75.9%
        28%
        3.1M
        91W-F_S30_R2_merged
        77.8%
        26%
        3.1M
        91W-G_S1_R1_merged
        62.3%
        28%
        0.3M
        91W-G_S1_R2_merged
        62.8%
        27%
        0.3M
        9W-F_S43_R1_merged
        39.4%
        31%
        0.2M
        9W-F_S43_R2_merged
        39.2%
        31%
        0.2M
        9W-G_S48_R1_merged
        53.6%
        28%
        0.3M
        9W-G_S48_R2_merged
        55.1%
        27%
        0.3M
        EL3-G_S44_R1_merged
        61.1%
        28%
        0.5M
        EL3-G_S44_R2_merged
        62.2%
        27%
        0.5M
        ELB1-F_S70_R1_merged
        41.6%
        28%
        0.1M
        ELB1-F_S70_R2_merged
        43.2%
        27%
        0.1M
        ELB1-G_S56_R1_merged
        63.4%
        28%
        0.5M
        ELB1-G_S56_R2_merged
        64.9%
        26%
        0.5M
        ELB14-G_S37_R1_merged
        65.5%
        27%
        0.5M
        ELB14-G_S37_R2_merged
        66.7%
        26%
        0.5M
        ELB2-G_S59_R1_merged
        63.0%
        28%
        0.4M
        ELB2-G_S59_R2_merged
        65.0%
        26%
        0.4M
        ELB4-F_S14_R1_merged
        77.4%
        27%
        2.4M
        ELB4-F_S14_R2_merged
        77.1%
        26%
        2.4M
        ELB6-F_S51_R1_merged
        74.4%
        27%
        1.1M
        ELB6-F_S51_R2_merged
        75.2%
        26%
        1.1M
        ELB6-G_S60_R1_merged
        59.5%
        28%
        0.2M
        ELB6-G_S60_R2_merged
        60.6%
        27%
        0.2M
        ELB9-G_S73_R1_merged
        73.4%
        28%
        1.9M
        ELB9-G_S73_R2_merged
        73.9%
        27%
        1.9M
        PLB1-G_S77_R1_merged
        63.3%
        28%
        0.5M
        PLB1-G_S77_R2_merged
        64.4%
        27%
        0.5M
        PLB14-G_S16_R1_merged
        50.0%
        29%
        0.1M
        PLB14-G_S16_R2_merged
        51.3%
        28%
        0.1M
        PLB15-F_S26_R1_merged
        68.8%
        27%
        0.6M
        PLB15-F_S26_R2_merged
        69.9%
        26%
        0.6M
        PLB15-G_S3_R1_merged
        70.0%
        26%
        1.3M
        PLB15-G_S3_R2_merged
        72.0%
        25%
        1.3M
        PLB2-F_S19_R1_merged
        74.3%
        28%
        1.4M
        PLB2-F_S19_R2_merged
        75.9%
        27%
        1.4M
        PLB2-G_S39_R1_merged
        63.1%
        27%
        0.7M
        PLB2-G_S39_R2_merged
        62.9%
        26%
        0.7M
        PLB4-F_S57_R1_merged
        73.5%
        28%
        2.9M
        PLB4-F_S57_R2_merged
        74.6%
        27%
        2.9M
        PLB4-G_S36_R1_merged
        61.6%
        28%
        0.6M
        PLB4-G_S36_R2_merged
        61.9%
        27%
        0.6M
        PLB6-G_S87_R1_merged
        34.6%
        28%
        0.0M
        PLB6-G_S87_R2_merged
        33.6%
        27%
        0.0M
        PLB7-F_S64_R1_merged
        76.1%
        26%
        2.3M
        PLB7-F_S64_R2_merged
        77.5%
        25%
        2.3M
        PLB7-G_S55_R1_merged
        59.6%
        28%
        0.4M
        PLB7-G_S55_R2_merged
        61.0%
        26%
        0.4M

        FastQC

        Version: 0.12.1

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        All samples have sequences of a single length (65bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        TGGAAGGGTAAGTAGATTTTGTTTTATATGTGGTATTTGTTGTGTTGTTT
        87
        635576
        0.4724%
        TGGTATGAGTTTGATAGTGGATAAGTATTGTGAGGGAAAGTTGAAAAGAA
        87
        669386
        0.4975%
        TGGATGTGGTTGTAAATTTGTATATTTTGTATAGTTAAATGGATGTTTTA
        87
        633644
        0.4709%
        TGGTAGTAAAATTTGTGTTAAAGTGGGGTGTTTGTTTGGTTGTGTGGGAT
        87
        437141
        0.3249%
        TGGGAGTTTAATTTTAGAATTGAGGAGTTTGTGTTTTGTTTTTTGTTTAA
        87
        467558
        0.3475%
        TGGGTATGAAATATTGGTTTAGAGATGTAGGTAAAAATTAGTTGTATGGT
        87
        345270
        0.2566%
        TGGATTTGTAATAATATAAGTAATATGATGGGTGTTATATGTGGAGTAGG
        87
        386855
        0.2875%
        TGGTGTGTTGAAAAGATGTGTAAATTTGAATGTTTAGAGGAAGTAAAAGT
        87
        351997
        0.2616%
        TGGTAGTAAAATTTTTGTTAAAGTGGGGTGTTTGTTTGGTTGTGTGGGAT
        87
        304323
        0.2262%
        TGGATTGTATTTATATTTGTAGTAGGTTTTTAAGGTGTATAGTTTTTAGT
        87
        267719
        0.1990%
        CAAACATAACTACAAATTTATACATCCCACACAACCAAACAAACACCCCA
        87
        871498
        0.6477%
        CAAACCAACTTTACAAATCCACCCATTTACCTCTAAACAATTTCACATAC
        87
        697648
        0.5185%
        CAAATTTATAATAACATAAACAACACAACAAATACCACATATAAAACAAA
        87
        587040
        0.4363%
        CAATAATAATCCTTCCACAAATTCACCTACAAAAACCTTATTACAACTTT
        87
        373367
        0.2775%
        CAAAACAACCTTTACAAAACATATCAAATACAATAATACCAACACTAATA
        87
        371761
        0.2763%
        CAACACATTTAAAATACCACTACTTTTATCATTTCTTTACTTATTCAATT
        87
        482620
        0.3587%
        CAACAATAAAACCCATACTAAAATAAAACATCCATTTAACTATACAAAAT
        87
        345373
        0.2567%
        CAAAAAAATAAACAAATCCTACTCCACATATAACACCCATCATATTACTT
        87
        442572
        0.3289%
        CAACAATAAAACCCTTACTAAAATAAAACATCCATTTAACTATACAAAAT
        87
        221690
        0.1648%
        CAAAATTCAAACTCATACTACTAAAATATCATAACACCAAATCACCTACA
        87
        199671
        0.1484%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1